A bioinformatics classifier and database for heme-copper oxygen reductases

• Published in: PloS one 2011-04, Vol.6 (4), p.e19117-e19117
• Main Authors: Sousa, Filipa L, Alves, Renato J, Pereira-Leal, José B, Teixeira, Miguel, Pereira, Manuela M
• Format: Article
• Language: English
• Subjects: Amino acids; Automation; Bacterial Proteins - chemistry; Bioinformatics; Biology; Chemistry; Classification; Classifiers; Computational biology; Computational Biology - methods; Computer Science; Copper; Copper - chemistry; Cytochrome; Databases, Protein; Enzymes; Eukaryotes; Genome; Genomes; Genomics; Heme; Heme - chemistry; Homology; Information processing; Markov analysis; Mitochondria; Models, Molecular; Nitric oxide; Oxidoreductases - classification; Oxygen; Oxygen reductase; Phylogenetics; Prokaryotes; Protein Conformation; Protein Structure, Tertiary; Proteins; Protons; Reductases; Respiration; Sequence Alignment; Sequences; Software; Trends
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0019117

Heme-copper oxygen reductases (HCOs) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). The number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of HCO sequences. These enzymes were initially classified into three different types being this classification recently challenged. We reanalyzed the classification scheme and developed a new bioinformatics classifier for the HCO and Nitric oxide reductases (NOR), which we benchmark against a manually derived gold standard sequence set. It is able to classify any given sequence of subunit I from HCO and NOR with a global recall and precision both of 99.8%. We use this tool to classify this protein family in 552 completely sequenced genomes. We concluded that the new and broader data set supports three functional and evolutionary groups of HCOs. Homology between NORs and HCOs is shown and NORs closest relationship with C Type HCOs demonstrated. We established and made available a classification web tool and an integrated Heme-Copper Oxygen reductase and NOR protein database (www.evocell.org/hco).